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Analytical chemistry (分析化学)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

[ protocol | unit | culture | validation ]

Analytical purposes

Quantitative analysis ≈ measurement

Lord Kelvin (1824-1907) "If you cannot measure, your knowledge is meager and unsatisfactory."

Qualitative analysis
State analysis


Inorganic analysis
Organic analysis

Absolute amount of samples

Macro analysis: 0.1-several g
Semi-micro analysis: 10-100 mg
Micro analysis: 1-10 mg
Ultra-micro analysis: < 1 mg

Relative amount of objects

Macro determination: 100ppm-100%
Major constituent determination: 1-100%
Minor constituent determination: 0.01-1%
Micro/trace determination: < 100ppm


Chemical microsensors and microinstrumentation

CHEMFETS (ISFET): Merits = small size (e.g., less than 1 mm² area), low output impedance, in vivo monitoring, small sample volumes, multiple-ion sensor arrays
The CHEMIST is essentially a conventional insulated-gate field effect transistor that has its metallic gate contact replaced by a chemically sensitive coating and a reference electrode.
Ion-controlled diodes
This device is a combination of a p-n junction and a metal oxide semiconductor capacitor in which the junction makes contact with the inversion layer of the capacitor. Like CHEMFET, the device can be use as an ion sensor by application of a suitable ion-selective coating to the gate surface.
Schottky diodes
In its simplest form Schottky diode consists of a small area of metal contact with a semiconductor. This contact exhibits a rectifying behavior and a characteristic nonlinear current-voltage dependence.
In the case of organic semiconductors the use of such compounds as vapor sensors has been hindered by the rather high resistivities of the material (e.g., 108-1015 ohm·cm).
Thin-film tin oxide gas sensors
Tin oxide and other metal oxide semiconductor are sensitive to low concentration of vapors. In operation a sintered block of the semiconductor is heated to several hundred degrees centigrade and its electrical conductivity is monitored.
The device, presently manufactured by Micromet, consists of a planer interdigital microelectrode array, one side of which is attached as a floating gate to an onchip FET charge amplifier. The other side of the microelectrode array is driven with a sinusoidal voltage. By measuring the amplitude and phase differences of the signal applied to the driven gate and the signal produced by floating gate, it is possible to determine the complex impedance (i.e., the resistance and capacitance) of the medium in contact with the electrode. The integration of the FET amplifier and microelectrode permits extremely weak currents to be measured easily.

Porous carbon packings for liquid chromatography

Table 1. Comparison of properties of carbon and reversed-phase silica packings

PropertyReversed-phased silicaCarbon
Surface functional groupsn-Alkyl, alkylaryl, aryl, residual hydroxyisAromatic-type acidic and basic functional groups
Specific surface area100-200 m²/g5-1000 m²/g
Type and extent of particle porosityOpen pores 60-80%Open and closed pores 30-60%
Mean pore size and pore size distribution5-25 nm


1-1000 nm

micro-, meso-, macropores

significant figures or effective digits (有効数字, sf)

Digits being effective to its measurement resolution

Protocol (プロトコル)

A defined procedures, that can be assessed by anybody, for experiments and measurements.

Chromatography (クロマトグラフィ)

Clinical analysis (臨床分析)

The improvement of sensitivity and specificity on chromatography Clinical analysis
Fig. Connection to mass spectrometer

Clinical analysis

Fig. 3. Immunoassay test principle. The immunoassay reaction is a result of competition between tagged analyte (A*) and unlabeled analyte (A) for a limited number of binding sites on the antibody (Y). As a result of the competitive reaction, the tagged analyte is partitioned between the fraction bound to antibody and the fraction free in solution.

(Chait & Ebersole 1981)

[ Qunatification | Markers on litter decomposition ]

Phospholipid fatty acids (PLFAs)

Protocol for the quantification

Extraction of total lipids

5 g soil (powderization, if required)
↓ + 21:0 (internal standard material, I.S.) in benzene solution
↓ + 10 ml methanol
↓ + 5 ml chloroform
↓ + 4 ml water or buffer solution (citric acid or phosphoric acid)
∇ vortex (5 min)
∇ leave at rest (5 min)
↓ + 5 ml chloroform
∇ vortex (1 min)
↓ + 5 ml water or buffer solution (1:1:0.9)
∇ vortex
∇ 3000 rpm for 5 min.

In the test tube
H2O/Methanol fraction
Chloroform fraction ← recover lipid by a Pasteur pipette
Debris (soil/litter)

↓ + 5 ml chloroform
∇ vortex
∇ ← recover chloroform fraction
↓ put the fractions together
total lipid

Separation of PLFAs from total lipids

chloroform fraction (= total lipid)
silicic acid chromatography
↓methanolysis + 2nd I.S.
total fatty acid/g soil

Identification and quantification of PFLAs

If molecular species can not be identified, the species is determined by a gas chromatograph mass spectrometer (so-called GC mass)

Extraction and fractionation (抽出・分画)

Centrifugation (遠心分離)

= centrifugal separation
Principle: separation by using density difference - not by the mass
i) centrifugal force, fr

fr = mrω2

m: particle mass (kg)
r = radial distance from center point (m)
ω = angular velocity = /dt (rad/s)

G: relative centrifugal force, RCF = mrω2/mg = 2/g
N: revolutions per minute, rpm

Centrifugal (遠心分離器)
= centrifugal machine, centrifugal precipitator, centrifugal separator, centrifuge, centrifuge machine or centrifuge separator
Swing-out roter 104/min_______Fixed angled roter: 2 × 105/min

rmax - rmin_______________rmax - rmin

Suspension: the mixed material added into the centrifuge tube
Pellet (precipitate): hard-packed concentration of particles after centrifugation
Supernatant: clarified liquid above the precipitate
Separation of ER
homogenatet cells
┃ centrigugate with 800-1000 × g, 5-10' + 0.2-0.4 M sucrose
┣━━━━━━━━━━━━━━━━┓_____⇑ not break organella
ppt (nuclei, chloroplast)_____supernatant
┏━━━━━━━━━━━━━━━━┫ 10000-15000 × g, 15-20'
ppt (mitochondria)_________supernatant = post-mitochondrial fraction
┏━━━━━━━━━━━━━━━━┫ 24000-40000 × g, 20-30'
ppt (r-ER + microsome)_____supernatant
┏━━━━━━━━━━━━━━━━┫ ultracentrifuge with
━━━━━━━━━━━━━━━━┃ 102000-105000 × g, 2 hr
ppt (free ribosomes polysomes) supernatant = S100 fraction
Furthermore, ribosomes are separated from r-ER by the separation the additon of deoxycholate-N (DOC), Nonidet P40 (NP40), polyethylene cethylethen (Bry 58) or Triton-X100 that uncouples lipids in r-ER
*: g vs rpm = revolution per minutes
S: unit of centrifugal separation

Proteins (タンパク質)

Purification and assay of enzymes (酵素の精製と分析)

D-Glycerate dehydrogenese purified from spinach leaves (EC D-Glycerate NAD oxidoreductase)
COOH-CHOH-CH2OH (D-glycerate) + NAD+ ⇔ COOH-CO-CH2OH (Hydroxypyruvate) + NADH + H+
Figure out enzyme purification techniques and enzyme characteristics.
I. Purification procedure
Fresh spinach (Spinacia oleracea L.) leaves (ca. 1 kg)

↓ 0.001 M 1-litter EDTA (pH 8.0)
Homogenize in a warming blender
Filtrate with three layers of gauze cloth
Centrifuge at 4,000 rpm for 10 min.

↓ - Fraction I

Add 13.3 g of AmSO4/100 ml of sup. with gentle
↓ stirring
After 15 min., centrifuge at 4,000 rpm for 20 min., discard ppt
Add 15 g of AmSO4/100 ml of sup. with gentle
↓ stirring
After 15 min. centrifuge at 4,000 rpm for 20 min.
Dissolve ppt with 300 ml of 0.02 M phospate buffer (pH 6.0)

↓ - Fraction II

Adjust pH at 4.85 with addition of 1 N acetic acid 10-20 h under cold (4°C)
Centrifuge at 8,000 rpm for 20 min., discard ppt

↓ - Fraction III

Add 12.1 g of AmSO4/100 ml of sup. with gentle stirring
After 15 min., centrifuge at 8,000 rpm for 20 min., discard ppt
Add 7.9 g of AmSO4/100 ml of sup. with gentle stirring
After 15 min., centrifuge at 8,000 rpm for 20 min., discard sup.
Dissolve ppt with 0.001 M 100-ml EDTA (pH 7.9) - 0.0001 M 2-mercaptoethanol (for SH)

↓ - Fraction IV

Dialyze the sample against 5 l of the same buffer for 3 hr with 2 changes of buffer
↓ (discard ppt by centrifugation)
After dialysis, dilute the sample with equal volume of deionized water
Add 0.5 volume of calcium phosphate gel

↓ - Fraction V

Stir slowly for 15 min.
Centrifuge at 5,000 rpm for 15 min. and collect the gel
Elude enzyme from the gel with equal-volume sup. of 0.15 M phosphate buffer (pH 6.0)
↓ stir for 30 min.
Centrifuge at 5,000 rpm for 15 min., discard ppt

↓ - Fraction VI

Add 25 g of AmSO4/100 ml of sup.
After 30 min., centrifuge at 10,000 rpm for 20 min.
Dissolve ppt with small volume of 0.01 M phosphate buffer (pH 6.0)

↓ - Fraction VII


Table 1. Protein concentration in each fraction. C = concentration
    Fraction# Dilution  1st   2nd   3rd    C (mg/ml)
    I         ×   100  0.520 0.538 0.533   9.533
    II        ×   200  0.485 0.455 0.470  16.53
    III       ×   100  0.281 0.299 0.290   4.733
    IV        ×    40  0.304 0.320 0.312   2.052
    V         ×    10  0.380 0.390 0.385   0.660
    VI        ×    10  0.200 0.208 0.204   0.307
    VII       ×   100  0.210 0.208 0.209   3.133
II. Enzyme assay
Ly-hydroxypruvate 0.008 M (pH 6.0)  0.25 ml
NADH              1 mg/ml           0.2 ml
Ammonium sulfate  0.4 M             0.5 ml
Phosphate buffer  0.6 M (pH 6.0)    1.0 ml
Enzyme (sample)                       0.1 ml
Deionized water
Final volume                          3.1 ml
Enzyme dilution buffer: 0.01 M phosphate buffer (pH 6.0)
Results (Table 1)
I. Protein concentration in each fraction
II. Enzyme activity
When a sample is too dense to measure the concentration, re-measurement should be conducted after the dilution.
Measure NADH-NAD+ activity. Ex. NAD oxydase: NADH + O2 - NAD+ in 1 ml reactive solution (Table 2)
Measurement of Km
Fraction #VII was diluted to 1/2, 1/4, 1/8, 1/10, and 1/16, using 0.008 M substrates. Thereafter, measure the activities by the enzyme assay described above. (Results, omitted)
Thermal inactivation (熱失活)
Methods: Treat Fraction VII at 40°C for 10, 20, 40 and 80 min, and at 50°C for 1, 2, 3, 4, and 5 min. Measure the activities by enzyme assay method described above
Effect of salt on enzyme activity (塩の効果)
Methods: Measure reaction pace by various salts, i.e., KCl and NaCl, (0.4 M) with different soaking periods (0, 30, 60, 90, 120, 180, and 210 min., if possible soak longer time) and cmpare with (NH4)2SO4
Table 2. Results. SA = specific activity (units/ml·protein)
  Frac-  Volume  Protein  Activity   SA     Purifi-  Yield
  tion#  (ml)    (mg/ml)  (unit/ml)         cation   (%)
  I      232      9.533    5.114     0.5365   1.0  100.0
  II      50     16.53    19.27      1.1658   2.17  81.2
  III     45.5    4.733   18.625     3.9351   7.33  71.4
  IV      17      2.052   14.6       7.1150  13.26  20.9
  V       34      0.660    3.515     5.3258   9.93  10.1
  VI       ?      0.303    1.515     4.9349   9.20   ?
  VII      3      3.133   17.7       5.6495  10.53   4.5


1. Quantitative analysis of nitrogen

UV absorbance = adjust at 280 nm Absorbance

Ex. Aromatic amino acid: phenylalanine: 250 nm = 190 mol Ab., Tryptophane: 278 nm = 5500 mol Ab., Trypsin: 275 nm = 1340 mol Ab.

2. Turbid method: acidic - low solubility

Sample: protein 0.5-1.5 mg/ml + 1.25% TCA (Trichloroacetic acid) 4 ml

3. Lowry's method: Phenol reagent

A: 2% Na2CO3 with 0.1N NaOH
B: 1% CuSO4·5H2O
C: 1% Na-tartrate or 1% K-tartrate
D: = B + C (1:1)
E: = A + D (50:1)

D and E should be prepared just before the using (within 24 hr), because those are unstable solution.

F: phenol reagent 1N


sample (5-100 g protein) 0.6 ml
add 3.0 ml E ← agitation ← placing them for 10 min ← add 0.3 ml F ← agitation ← place them for 30 min
measuring at Ab750 (or Ab500)
Inhibitors on the measurement of Lawry's method: EDTA, AuSO4, Thial reagents, K+ ion, Glycerol, Triton X-100, etc.

4. Bradford's method (Analytical Biochemistry, 1976, 72, 248-252)

Dry reagent (ドライ試薬)

(Walter 1983)

Dry reagent chemistries in clinical analysis

Dry reagent chemistry
progress of quantitative measurments based on analytical chemistry on iatrochemistry

19c: invented litmus paper 1970s': developed dry reagent chemistry for measuring blood elements quantitatively

Dry reagent Dry reagent chemistry: small amount of samples can be handled only by one step, monitored by samll apparatus ← cheap

↔ Large amount of samples by several steps on many medical examinations

Components in dry reagent carrier

types of chemical reaction monitored
effectivness of supplied carrier

Dry reagent
Fig. 1. Basic components of dry reagent chemistry carriers.

Enzyme immunoassay (酵素免疫測定法)

(Abbreviations: RIA = radioimmunoassay, FIA = fluorescent immunoassay, ELISA = enzyme-linked immuoassay, EMIT = enzyme-multiplied immunoassay)
Table 1. Immunoassay comparison
              RIA               FLA           EIA
Sensitivity   High (ng-pg)      High (ng-pg)  High (ng-pg)
Specificity   High              High          High
Speed         Days              Days          Hours
Reagents      Short shelf       Reasonable    Long shelf
                life              shelf life    life
Equipment     Scintillation or  UV monitor    Spectro-
    required    gamma counter                   photometer
Personnel     Skilled with        Skilled     Minimal
                license                         training
Cost          $7/test           $5/test       $2/test
Table 2. EIA comparison

Heterogeneous assay ↔ Homogeneous assay
Reagent separation required (centrifugation or filtration) ↔ Reagent separation not required
Reagent washings required ↔ Step washings not required
Slower than EMIT ↔ Faster than ELISA
Sensitivity greater than EMIT ↔ Sensitivity less than ELISA
Macromolecules measured (antigens, antibodies) ↔ Measures small molecules (haptens*)
For diagnosing infectious diseases, immunoglobulins ↔ For drug, hormone, metabolite determinations
Solid phase assay ↔ Liquid phase assaya

* hapten (ハプテン, 付着体): small molecules that elicit an immune response only when attached to a large carrier such as a protein Ex. urushiol

immunoassay Fig. 5. EMIT instrumentation

Polystyrene tube coated with antigen ← Incubate at 37°C ← Wash 3X ← Serum added ← Incubate at 37°C ← Wash 3X ← Enzyme-labeled antiserum added ← Incubate at 37°C ← Wash 3X ← Substrate added ← Visible color change ← Spectrophotometer absorption readings

Fig. 6. ELISA steps for serodiagnosis of diseases

Spectrophotometry (分光光度法)

High-sensitivity spectrophotometry

Table 1. Absorption detection limits in solution

Method_________________Detection limit (M)
Conventional transmission___1 × 10-5
Laser intracavity___________5 × 10-6
Interferometry_____________1 × 10-7
Photothermal deflection_____1 × 10-7
Photoacoustic_____________1 × 10-7
Thermal lens______________8 × 10-8

Table 2. Spectrophotometric methods

Conventional spectrophotometry__Thermocouple
Wavelength modulation_________Thermal lens
Laser intracavity_______________Phtoacoustic

Table 3. Criteria for comparison of spectrophotometric methods

Instrumental factors_____Sample factors
Tuning range__________Solvent physical properties
Pathlength effects_______Solvent absorbance
Reflection losses_______Molecular scatter
Flow effects___________Particulate scatter

Fig. 1. Experimental arrangement for filling and taking spectra with long hollow fibers. Source spectral light coupling correction is made by first recording a spectrum with a long fiber and then removing all but a small length and recording again. The difference is the transmission spectrum of the filled hollow fiber.
|– Gain Reference loss Samples loss –|– Detector
Fig. 2. Schematic configuration for quantitative intracavity absorption enhancement measurements. M1, M2 are mirrors.

Photon plumbing

Fiber optics (FO), waveguides, and evanescent waves as tools for chemical analysis
Optical wave guide (光導波路) - optic(al) fiber (fiberoptics, 光ファイバー)
Optical fiber: dielectric line for visible and near-infrared wavelengths

circular section of which refraction index is higher on the center than on the margin ← the light is walled in the fiber
flexible, transparent fiber made by drawing glass (silica) or plastic

  1. Single mode fiber (単一モードファイバー): diameter of center (core) = several μm, used for long distance
  2. Multimode fiber (多モードファイバー): diameter of center (core) = several tens μm, used for short distance
Fiber optics
Fig. 1. The geometrical path of light passing through a section of optical fiber. The index of refraction of the surroundings, the fiber cladding, and the fiber itself are denoted by n1, n2, and n3, respectively. If the path of the light shown enters at the greatest angle of acceptance of the fiber, then n1sinθ = NA is the numerical aperture of the fiber. In terms of the modes, the case shown corresponds to a high-order mode (light entering far off-axis).
Fiber optics
Fig. 2. The relationship between field intensity and transverse distance from the center of a symmetric waveguide is illustrated for the first three modes. The fields have an exponentially decreasing value beyond the surface of the waveguide. Outside the waveguide, the higher order modes have a greater intensity at a given distance than do lower order.
Fiber optics
Fig. 3. The path of a beam totally reflected within a prism and the associated evanescent field is illustrated. The index of refraction of the sample is less than that of the prism. In the lower part of the figure, the dependence of intensity on distance, y, from the interface is shown and the penetration depth, dp, is indicated.

PCR (polymerase chain reaction)

Terminal Restriction Fragment Length Polymorphism (T-RFLP) Protocol

Preparing a sample for T-RFLP analysis is a two step process. First, PCR amplify the desired region of DNA using a HEX labeled forward primer and/or a FAM labeled reverse primer. Second, digest the PCR product with one or more restriction enzymes. The details of this process follow.
PCR amplify DNA using labeled primer(s)
Working concentrations of components:
    Component                  Working concentration
    Unlabeled forward primer             10 μM
    Unlabeled reverse primer             10 μM
    HEX labeled forward primer           10 μM
    FAM labeled reverse primer           10 μM
    PerkinElmer PCR Buffer II            10X 
    PerkinElmer MgCl2 Solution           25 mM
    dNTP's                                2 mM (each)
    BSA                                  20 mg/mL
    PerkinElmer AmpliTaq DNA Polymerase   5 U/μL
Volumes (μL) of components per reaction using working concentrations noted above:
    Component        25 μL   50 μL   75 μL  100 μL
    Forward primer    0.50     1.00     1.50     2.00
    HEX forward pr.*  0.75     1.50     2.25     3.00
    Reverse primer    0.50     1.00     1.50     2.00
    FAM reverse pr.*  0.75     1.50     2.25     3.00
    Buffer            2.50     5.00     7.50    10.00
    MgCl2             3.75     7.50    11.25    15.00
    dNTP's            2.50     5.00     7.50    10.00
    BSA               0.05     0.10     0.15     0.20
    milliQ H2O       13.35    26.70    40.05    53.40
    Taq               0.10     0.20     0.30     0.40
    Template          1.50     3.00     4.50     6.00

* NOTE: Run separate PCR reactions for each labeled primer (i.e., run HEX labeled forward primer with unlabeled reverse primer; run FAM labeled reverse primer with unlabeled forward primer).

Using the parameters above, amplify DNA using labeled primer(s)
Check PCR product by agarose gel electrophoresis

- If positive, purify product
- If you have both HEX and FAM labeled product, purify separately and keep them separate until digestion (see below)

Digest the PCR product
Working concentrations of components:
  Component                    Working concentration 
  Labeled PCR product*        250-300 ng (each) per digest
  GibcoBRL REact buffer        10X
  (restriction enzyme specific)
  GibcoBRL restriction enzyme  10 U/μL
  milliQ H2O                   na

* NOTE: If you have both HEX and FAM labeled product, combine 250–300 ng of each labeled product in a single digest (i.e., 250 – 300 ng of HEX labeled product combined with 250–300 ng of FAM labeled product to give a total of 500–600 ng of labeled product in a 20 μL digest)

Volumes (μL) of components per digest using working concentrations noted above:
    Component            Volume (20 μL digest)
    Labeled PCR product  depends on PCR product
    Buffer               2.00
    Restriction enzyme   1.50
    milliQ H2O           dilute digest to 20 μL
                         (PCR product + H2O = 16.5 μL
                         + buff. + re. enz. = 20 μL)

Digest purified PCR product with preferred restriction enzyme(s)

- If digesting with multiple restriction enzymes, do a separate digest for each restriction enzyme

Digested product is ready for T-RFLP analysis

Protocol provided by Brian Wade at the MSU Center for Microbial Ecology

Unit (単位)

International System of Units, SI (国際単位系)

SI The seven SI base units
kelvin (temperature)
second (time)
meter (length)
kilogram (mass)
candela (luminous intensity)
mole (amount of substance)
ampere (electric current)
Metric system (メートル法)
1 mm = 1/1000 m
1 μm = 1/1000 mm
1 nm = 1/1000 μm
1 Å = 1/10 nm
Cardinal numbers (基数)
100:___________ one hundred
101:___________ one hundred (and) one
1,000:__________one thousand
100,000:________one hundred thousand
30,000,000,000:__three followed by ten zero
1,000,000:_______ one million
1,000,000,000:____one billion
1,000,000,000,000: one trillion
1015:____________one quadrillion
1018:____________one quintillion
1021:____________one sextillion
1024:____________one septillion
1027:____________one octillion
1030:____________one nonillion
1033:____________one decillion
1010: one followed by ten zeros (ten to the tenth)

[ plant culture | references ]

Culture (カルチャー)

  • cultivation, tillage (biology, including ecology)
  • the other meanings are omitted

Plant culture

Medium for water culture (hydroponics). Observation points: pH, leaf colors, and dry weight
Fe2(SO4)3 2%3 dp3 dp3 dp3 dp--

A house that allows plant growth even in fields
Toolik House


A closed system that regulates various environments used for investigating plant growth

Validation (バリデーション, 検証)

An act, process, or instance of validating; especially : the determination of the degree of validity of a measuring device

(Merrian-Webster Online)

Importance of validation

Fig. Basic concept of the validation process like a balance.


Technique: scientific principle useful for providing compositional information


Procedure: Distinct adaptation of a technique for a selected measurement purpose

Pararosaniline method for measurement of sulfur dioxide

Method: Written directions necessary to use a method

ASTM D2914 - Standard Test Method for the Sulfur Dioxide Content of the Atmosphere (West Gaeke Method)

Protocol: Set of definitive directions that must be followed, without exception, if the analytical results are to be accepted for a given purpose

EPA Reference Method for the Determination of Sulfur Dioxide in the Atmosphere (Pararosaniline Method)

Fig. Collaborative test process. Test
Fig. 3. General process for evaluation/validation of methodology.


  • Bligh EG, Dyer WJ (1959) A rapid method for total lipid extraction and purification. Can. J. Biochem. Physiol. 37: 911-917
  • Fiske CH, SubbaRow YJ (1925) The colorimetric determination of phosphorus. J. Biol. Chem. 66: 375-400
  • White DC, Davis WM, Nickels JS, King JD, Bobbie RJ (1979) Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oceologia 40: 51-62